The problem is with the monitor. Since the monitor is analog, you have to physically turn the pots to get the right settings. Each resolution requires different settings. So to get the right settings on several resolutions at once, an analog monitor would have to somehow move the pots itself to get the right settings automatically. Obviously this can't be done.
The only way to prevent this, assuming you don't want to fiddle with the pots every time you change resolutions, is to force the desktop, your front end, and all games to run at a single resolution. Beyond that, you could always spend some coin on a digital monitor it will remember your settings for every resolution.